Comments (3)
Hi,
It seems that there are no splicing events have been reported in the initial .dice file, hence the sorting failed. Do you only have five splicing events and all of them can't be fetched? BTW, could you also check if the chromosome id matches between GTF and bam files, e.g., KV466212.1.
Yuanhua
from diceseq.
Hello,
Thank you for your advice. I switched to a different annotation file to make sure it matches the bam files. However, I am now getting a new error. I checked and it seems to have the right "ensembl like" format.
diceseq -a XENTR_9.1_Xenbase.gff3 $my_sam_list -t 6,8,10,13,16,24 -o out_file
[DICEseq] loading annotation file...Traceback (most recent call last):
File "/users/sk1350/.conda/envs/diceseq_env/bin/diceseq", line 8, in
sys.exit(main())
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/diceseq.py", line 121, in main
genes = loadgene(options.anno_file)
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/utils/gtf_utils.py", line 234, in loadgene
if aLine[0] != _gene.trans[-1].chrom:
IndexError: list index out of range
from diceseq.
Hi,
Indeed, it looks the issue comes from the GTF format incompatibility. It requires format as: gene --> transcript 1 --> exon1 --> exon2 ... -> transcript 2 exon1 --> exon3 ....
Example is here: http://diceseq.sourceforge.net/manual.html#annotation-format
Best,
Yuanhua
from diceseq.
Related Issues (5)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from diceseq.